[BioC] Using ChromHeatMap with the org.Mm.eg library

[Tim Rayner]

Dear Mike,

Thanks for your email, and thanks to Marc for stepping in so promptly.
Marc's analysis is quite correct - the makeChrStrandData function
needs the row names of your data matrix to correspond to the probe or
gene identifiers used by the annotation library package. In the case
of org.Mm.eg.db the row names should correspond to Entrez IDs. The
package was originally written for chip-based data but there's no
reason it shouldn't also work in your case. I'll update the
documentation to make that a bit clearer.

Best regards,

Tim Rayner



On 19 August 2010 17:15, Michael Muratet <mmuratet at hudsonalpha.org> wrote:
> Greetings
>
> I am attempting to make a ChromHeatMap from RNA-seq data with Entrez IDs
> using org.Mm.eg for annotation. The original data was aligned to the UCSC
> knownGenes table and I can map the original identifiers to just about any
> other system using the browser tables. I tried
>
>> chrData <- makeChrStrandData(matrix(neuro.ca.7d), lib="org.Mm.eg")
> Error in makeChrStrandData(matrix(neuro.ca.7d), lib = "org.Mm.eg") :
>  Error: Data matrix must have row names corresponding to probe IDs.
>
> I suspect that I'm missing a step somewhere but I can't find it in the
> documentation. Is there a way to get the annotation from the org.Mm.eg data?
>
> Thanks
>
> Mike
>
> Session info:
>
> R version 2.11.0 (2010-04-22)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] ChromHeatMap_1.2.0                 hgu95av2.db_2.4.1
>  [3] org.Hs.eg.db_2.4.1                 ALL_1.4.7
>  [5] org.Mm.eg.db_2.4.1                 RSQLite_0.8-4
>  [7] DBI_0.2-5                          BSgenome.Mmusculus.UCSC.mm9_1.3.16
>  [9] BSgenome_1.16.5                    Biostrings_2.16.7
> [11] GenomicRanges_1.0.5                IRanges_1.6.8
> [13] vsn_3.16.0                         limma_3.4.4
> [15] gplots_2.7.4                       caTools_1.10
> [17] bitops_1.0-4.1                     gdata_2.7.1
> [19] gtools_2.6.1                       DESeq_1.0.4
> [21] locfit_1.5-6                       akima_0.5-4
> [23] geneplotter_1.26.0                 lattice_0.18-5
> [25] annotate_1.26.1                    AnnotationDbi_1.10.0
> [27] Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] affy_1.26.1           affyio_1.16.0         genefilter_1.30.0
> preprocessCore_1.10.0
>  [5] RColorBrewer_1.0-2    RCurl_1.3-1           rtracklayer_1.8.1
> splines_2.11.0
>  [9] survival_2.35-8       tools_2.11.0          XML_2.8-1
> xtable_1.5-6
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
>
>
>
>
>